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correct nonPBC vs PBC calls to PySCF

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This commit is contained in:
Steve Plimpton
2023-01-31 13:31:42 -07:00
parent b4ac95b225
commit 7c9068c34a
3 changed files with 14 additions and 15 deletions
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4
examples/QUANTUM/PySCF/README
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@ -107,8 +107,8 @@ Step 4: run the 2-water QMMM problem for a few steps
# Run with MPI: 1 proc each # Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.pyscf.qmmm.mpi.1 -in in.water.pyscf.qmmm : -np 1 python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method MPI" -pbc yes % mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.pyscf.qmmm.mpi.1 -in in.water.pyscf.qmmm : -np 1 python pyscf_mdi.py -mdi "-name PYSCF -role ENGINE -method MPI" -pbc no
# Run in plugin mode: 1 proc # Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/work_qm" -log log.water.pyscf.qmmm.plugin.1 -in in.water.pyscf.qmmm.plugin % lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/PySCF" -log log.water.pyscf.qmmm.plugin.1 -in in.water.pyscf.qmmm.plugin

2
examples/QUANTUM/PySCF/in.water.pyscf.qmmm.plugin
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@ -46,4 +46,4 @@ thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
thermo 1 thermo 1
mdi plugin pyscf_mdi mdi "-role ENGINE -name PySCF -method LINK" & mdi plugin pyscf_mdi mdi "-role ENGINE -name PySCF -method LINK" &
extra "-pbc yes" command "run 2" extra "-pbc no" command "run 2"

23
examples/QUANTUM/PySCF/pyscf_mdi.py
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@ -1,9 +1,11 @@
# MDI wrapper on PySCF quantum code # MDI wrapper on PySCF quantum code
# NOTE: Qs or issues to still address # Todo:
# mm_radii is input to PySCF in Angstroms? # allow for changes in box size on driver side, e.g. NPT
# should just work for PySCF
# NOTE: Qs or issues to still address for PySCF support
# add list of radii for all elements # add list of radii for all elements
# allow for changes in box size, e.g. every step for NPT
# PySCF can do DIRECT mode (LATTICE commands) for QMMM # PySCF can do DIRECT mode (LATTICE commands) for QMMM
# can it also do POTENTIAL mode (Coulomb potential at QM atoms) # can it also do POTENTIAL mode (Coulomb potential at QM atoms)
# if so, add PySCF logic in evaluate() # if so, add PySCF logic in evaluate()
@ -12,8 +14,6 @@
# any other PySCF settings for users to set # any other PySCF settings for users to set
# are the 3 below good default values # are the 3 below good default values
# is wiping out dm_previous sufficient to make it a new system # is wiping out dm_previous sufficient to make it a new system
# should max_memory=10000 depend on # of MM or QM atoms
# doc what "mf" is in evaluate()
# add PySCF code for AIMD (no MM atoms) # add PySCF code for AIMD (no MM atoms)
# how to specify box for mixed BC, i.e. cell.dimension = 2 or 1 # how to specify box for mixed BC, i.e. cell.dimension = 2 or 1
# also need command-line options for those cases ? # also need command-line options for those cases ?
@ -28,7 +28,8 @@ import MDI_Library as mdi
from pyscf.gto import Mole from pyscf.gto import Mole
from pyscf.pbc.gto import Cell from pyscf.pbc.gto import Cell
from pyscf import qmmm from pyscf import qmmm
from pyscf.dft import RKS from pyscf.dft import RKS as RKS_nonpbc
from pyscf.pbc.dft import RKS as RKS_pbc
# -------------------------------------------- # --------------------------------------------
@ -529,9 +530,9 @@ def evaluate():
box_str = "%s\n%s\n%s" % (edge_vec,edge_vec,edge_vec) box_str = "%s\n%s\n%s" % (edge_vec,edge_vec,edge_vec)
box_str = box_str % \ box_str = box_str % \
(box_A[0],box_A[1],box_A[2],box_A[3],box_A[4],box_A[5],box_A[6],box_A[7],box_A[8]) (box_A[0],box_A[1],box_A[2],box_A[3],box_A[4],box_A[5],box_A[6],box_A[7],box_A[8])
print("BOX STR:",box_str)
print("ATOM STR:",atom_str) print("ATOM STR:",atom_str)
print("BOX STR:",box_str)
print("MM COORDS:",mm_coords) print("MM COORDS:",mm_coords)
print("MM CHARGES:",mm_charges) print("MM CHARGES:",mm_charges)
print("MM RADII:",mm_radii) print("MM RADII:",mm_radii)
@ -543,18 +544,16 @@ def evaluate():
cell = Cell() cell = Cell()
cell.atom = atom_str cell.atom = atom_str
cell.a = box_str cell.a = box_str
cell.max_memory = 10000
cell.basis = basis cell.basis = basis
cell.build() cell.build()
else: else:
mol = Mole() mol = Mole()
mol.atom = atom_str mol.atom = atom_str
mol.max_memory = 10000
mol.basis = basis mol.basis = basis
mol.build() mol.build()
# QMMM with QM and MM atoms # QMMM with QM and MM atoms
# mf = ??? # mf = mean-field object
# qm_pe = QM energy + QM/MM energy # qm_pe = QM energy + QM/MM energy
# QM energy = QM_nuclear/QM_nuclear + electron/QM_nuclear + electron/electron # QM energy = QM_nuclear/QM_nuclear + electron/QM_nuclear + electron/electron
# QM/MM energy = QM_nuclear/MM_charges + electron/MM_charges # QM/MM energy = QM_nuclear/MM_charges + electron/MM_charges
@ -563,8 +562,8 @@ def evaluate():
# dm = molecular orbitals (wave functions) for system # dm = molecular orbitals (wave functions) for system
if mode == QMMM: if mode == QMMM:
if periodic: mf = RKS(cell,xc=xcstr) if periodic: mf = RKS_pbc(cell,xc=xcstr)
else: mf = RKS(mol,xc=xcstr) else: mf = RKS_nonpbc(mol,xc=xcstr)
mf = qmmm.mm_charge(mf,mm_coords,mm_charges,mm_radii) mf = qmmm.mm_charge(mf,mm_coords,mm_charges,mm_radii)
if dm_previous_exists: if dm_previous_exists: